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1. Multi-view spectral graph convolution with consistent edge attention for molecular modeling

   https://doi.org/https://doi.org/10.1016/j.neucom.2021.02.025  

   Shang, C; Liu, Q; Tong, Q; Sun, J; Song, M; Bi, J (July 2021, Neurocomputing)

   null (Ed.)

   Although graph convolutional networks (GCNs) that extend the convolution operation from images to graphs have led to competitive performance, the existing GCNs are still difficult to handle a variety of applications, especially cheminformatics problems. Recently multiple GCNs are applied to chemical compound structures which are represented by the hydrogen-depleted molecular graphs of different size. GCNs built for a binary adjacency matrix that reflects the connectivity among nodes in a graph do not account for the edge consistency in multiple molecular graphs, that is, chemical bonds (edges) in different molecular graphs can be similar due to the similar enthalpy and interatomic distance. In this paper, we propose a variant of GCN where a molecular graph is first decomposed into multiple views of the graph, each comprising a specific type of edges. In each view, an edge consistency constraint is enforced so that similar edges in different graphs can receive similar attention weights when passing information. Similarly to prior work, we prove that in each layer, our method corresponds to a spectral filter derived by the first order Chebyshev approximation of graph Laplacian. Extensive experiments demonstrate the substantial advantages of the proposed technique in quantitative structure-activity relationship prediction. 

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2. Motif-Based Graph Representation Learning with Application to Chemical Molecules

   https://doi.org/10.3390/informatics10010008  

   Wang, Yifei; Chen, Shiyang; Chen, Guobin; Shurberg, Ethan; Liu, Hang; Hong, Pengyu (March 2023, Informatics)

   This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed in real applications. Existing graph neural networks offer limited ability to capture complex interactions within local structural contexts, which hinders them from taking advantage of the expression power of ARGs. We propose motif convolution module (MCM), a new motif-based graph representation learning technique to better utilize local structural information. The ability to handle continuous edge and node features is one of MCM’s advantages over existing motif-based models. MCM builds a motif vocabulary in an unsupervised way and deploys a novel motif convolution operation to extract the local structural context of individual nodes, which is then used to learn higher level node representations via multilayer perceptron and/or message passing in graph neural networks. When compared with other graph learning approaches to classifying synthetic graphs, our approach is substantially better at capturing structural context. We also demonstrate the performance and explainability advantages of our approach by applying it to several molecular benchmarks. 

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3. Dual Label-Guided Graph Refinement for Multi-View Graph Clustering

   https://doi.org/10.1609/aaai.v37i7.26057  

   Ling, Yawen; Chen, Jianpeng; Ren, Yazhou; Pu, Xiaorong; Xu, Jie; Zhu, Xiaofeng; He, Lifang (June 2023, Proceedings of the AAAI Conference on Artificial Intelligence)

   With the increase of multi-view graph data, multi-view graph clustering (MVGC) that can discover the hidden clusters without label supervision has attracted growing attention from researchers. Existing MVGC methods are often sensitive to the given graphs, especially influenced by the low quality graphs, i.e., they tend to be limited by the homophily assumption. However, the widespread real-world data hardly satisfy the homophily assumption. This gap limits the performance of existing MVGC methods on low homophilous graphs. To mitigate this limitation, our motivation is to extract high-level view-common information which is used to refine each view's graph, and reduce the influence of non-homophilous edges. To this end, we propose dual label-guided graph refinement for multi-view graph clustering (DuaLGR), to alleviate the vulnerability in facing low homophilous graphs. Specifically, DuaLGR consists of two modules named dual label-guided graph refinement module and graph encoder module. The first module is designed to extract the soft label from node features and graphs, and then learn a refinement matrix. In cooperation with the pseudo label from the second module, these graphs are refined and aggregated adaptively with different orders. Subsequently, a consensus graph can be generated in the guidance of the pseudo label. Finally, the graph encoder module encodes the consensus graph along with node features to produce the high-level pseudo label for iteratively clustering. The experimental results show the superior performance on coping with low homophilous graph data. The source code for DuaLGR is available at https://github.com/YwL-zhufeng/DuaLGR. 

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4. Edgeformers: Graph-Empowered Transformers for Representation Learning on Textual-Edge Networks

   Jin, Bowen; Zhang, Yu; Meng, Yu; Han, Jiawei (May 2023, The Eleventh International Conference on Learning Representations, {ICLR} 2023)

   Edges in many real-world social/information networks are associated with rich text information (e.g., user-user communications or user-product reviews). However, mainstream network representation learning models focus on propagating and aggregating node attributes, lacking specific designs to utilize text semantics on edges. While there exist edge-aware graph neural networks, they directly initialize edge attributes as a feature vector, which cannot fully capture the contextualized text semantics of edges. In this paper, we propose Edgeformers, a framework built upon graph-enhanced Transformers, to perform edge and node representation learning by modeling texts on edges in a contextualized way. Specifically, in edge representation learning, we inject network information into each Transformer layer when encoding edge texts; in node representation learning, we aggregate edge representations through an attention mechanism within each node’s ego-graph. On five public datasets from three different domains, Edgeformers consistently outperform state-of-the-art baselines in edge classification and link prediction, demonstrating the efficacy in learning edge and node representations, respectively. 

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5. Edge Prompt Tuning for Graph Neural Networks

   Fu, Xingbo; He, Yinhan; Li, Jundong (April 2025, International Conference on Learning Representations)

   Pre-training powerful Graph Neural Networks (GNNs) with unlabeled graph data in a self-supervised manner has emerged as a prominent technique in recent years. However, inevitable objective gaps often exist between pre-training and downstream tasks. To bridge this gap, graph prompt tuning techniques design and learn graph prompts by manipulating input graphs or reframing downstream tasks as pre-training tasks without fine-tuning the pre-trained GNN models. While recent graph prompt tuning methods have proven effective in adapting pre-trained GNN models for downstream tasks, they overlook the crucial role of edges in graph prompt design, which can significantly affect the quality of graph representations for downstream tasks. In this study, we propose EdgePrompt, a simple yet effective graph prompt tuning method from the perspective of edges. Unlike previous studies that design prompt vectors on node features, EdgePrompt manipulates input graphs by learning additional prompt vectors for edges and incorporates the edge prompts through message passing in the pre-trained GNN models to better embed graph structural information for downstream tasks. Our method is compatible with prevalent GNN architectures pre-trained under various pre-training strategies and is universal for different downstream tasks. We provide comprehensive theoretical analyses of our method regarding its capability of handling node classification and graph classification as downstream tasks. Extensive experiments on ten graph datasets under four pre-training strategies demonstrate the superiority of our proposed method against six baselines. 

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